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Enabled code to deal with hard-clipping adaptor sequence when processing reads in pileup in indel caller. Proven now that changes are minimal (4 less calls in NA12878 chr20, quals slightly different), minor changes in vcf fields in integration tests. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5679 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
delangel 2011-04-22 14:10:33 +00:00
parent e050d94df4
commit 600617a63c
3 changed files with 10 additions and 13 deletions
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11
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
View File

@ -48,19 +48,13 @@ import org.broadinstitute.sting.utils.sam.ReadUtils;
import java.util.*;
public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihoodsCalculationModel {
private final int maxReadDeletionLength = 3;
private final int HAPLOTYPE_SIZE;
private final int minIndelCountForGenotyping;
private final boolean getAlleleListFromVCF;
// todo - the following need to be exposed for command line argument control
private final double indelHeterozygosity = 1.0/8000;
boolean useFlatPriors = true;
private boolean DEBUG = false;
// todo -cleanup
private HaplotypeIndelErrorModel model;
private PairHMMIndelErrorModel pairModel;
private GenomeLoc lastSiteVisited;
@ -114,7 +108,10 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
for ( ExtendedEventPileupElement p : indelPileup.toExtendedIterable() ) {
SAMRecord read = p.getRead();
//SAMRecord read = p.getRead();
SAMRecord read = ReadUtils.hardClipAdaptorSequence(p.getRead());
if (read == null)
continue;
if(ReadUtils.is454Read(read)) {
continue;
}

6
java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
View File

@ -583,11 +583,11 @@ public class PairHMMIndelErrorModel {
}
}
for (SAMRecord read : pileup.getReads()) {
/* SAMRecord read = ReadUtils.hardClipAdaptorSequence(read);
for (SAMRecord pread : pileup.getReads()) {
SAMRecord read = ReadUtils.hardClipAdaptorSequence(pread);
if (read == null)
continue;
*/
if(ReadUtils.is454Read(read)) {
continue;
}

6
java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
View File

@ -27,7 +27,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
public void testMultiSamplePilot1() {
WalkerTest.WalkerTestSpec spec = new WalkerTest.WalkerTestSpec(
baseCommand + " -I " + validationDataLocation + "low_coverage_CEU.chr1.10k-11k.bam -o %s -L 1:10,022,000-10,025,000", 1,
Arrays.asList("a2218244df08dce96d04f8736a6de796"));
Arrays.asList("02481347a19d80e09538f2f6aa1be74a"));
executeTest("test MultiSample Pilot1", spec);
}
@ -248,7 +248,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -glm INDEL" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("ffeea8550a707871a68f6707159f4ea9"));
Arrays.asList("08b63c534a7e129e53cdd1527d51be5c"));
executeTest(String.format("test indel caller in SLX"), spec);
}
@ -277,7 +277,7 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
" -glm INDEL" +
" -L 1:10,000,000-10,500,000",
1,
Arrays.asList("897057070aa2e3651d91625a58c5ec4b"));
Arrays.asList("1d1ddad622dbee7e74550b5bb9d0928f"));
executeTest(String.format("test indel calling, multiple technologies"), spec);
}